SMTL ID : 6ogp.1

X-ray crystal structure of wild type HIV-1 protease in complex with GRL-063

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: K.14, I.15, G.16, G.17, L.63, E.65 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.17, A:L.63, A:E.65 EDO.3: 6 residues within 4Å: Chain B: K.14, I.15, G.16, G.17, L.63, E.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.17, B:L.63, B:E.65, B:E.65

2 x MJD: (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl {(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-[(2-methylpropyl)({2-[(propan-2-yl)amino]-1,3-benzoxazol-6-yl}sulfonyl)amino]butan-2-yl}carbamate(Non-covalent)

MJD.2: 27 residues within 4Å: Chain A: R.8, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Chain B: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 Ligands: MJD.4 23 PLIP interactions: 10 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:L.23, B:I.47, B:V.82, B:I.84, A:A.28, A:V.32, A:I.47, A:P.81, A:I.84 Hydrogen bonds: B:G.27, B:D.29, B:D.30, A:D.29, A:D.30, A:D.30, A:D.30 Water bridges: B:I.50, B:I.50, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25 Halogen bonds: A:R.8 MJD.4: 27 residues within 4Å: Chain A: L.23, D.25, G.27, A.28, D.29, D.30, I.47, G.48, G.49, I.50, V.82, I.84 Chain B: R.8, D.25, G.27, A.28, D.29, D.30, V.32, I.47, G.48, G.49, I.50, P.81, V.82, I.84 Ligands: MJD.2 24 PLIP interactions: 13 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:A.28, B:V.32, B:I.47, B:P.81, B:I.84, A:L.23, A:I.47, A:V.82, A:I.84 Hydrogen bonds: B:D.29, B:D.29, B:D.30, B:D.30, A:G.27, A:D.29, A:D.30, A:D.30 Water bridges: B:I.50, B:I.50, A:I.50, A:I.50 Salt bridges: B:D.25, A:D.25 Halogen bonds: B:R.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bulut, H. et al., Single atom changes in newly synthesized HIV protease inhibitors reveal structural basis for extreme affinity, high genetic barrier, and adaptation to the HIV protease plasticity. Sci Rep (2020)

Release Date

2020-04-08

Peptides

Protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protease

Related Entries With Identical Sequence